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Detailed information for vg1000621991:

Variant ID: vg1000621991 (JBrowse)	Variation Type: SNP
Chromosome: chr10	Position: 621991
Reference Allele: G	Alternative Allele: A
Primary Allele: A	Secondary Allele: G

Inferred Ancestral Allele: Not determined.

Flanking Sequence (100 bp) in Reference Genome:

ATGGTGCAGGAGGAGACGGCGAAGCCGGAGGAGATGGTGCACGAGACGCCGCTTGTCGCCCAGGGAGGATGATGTACCGCTTGCGCTATAGTATAATGGC[G/A]
TGCCTTGTGTCTCGTAGATGCGTCTCACCATCTCCTCCTAGGTAGTCCAACTCGAGGTCCTCGTACACGGCTTCCACCAGCTCAACTTCGACCCTCGAGT

Reverse complement sequence

ACTCGAGGGTCGAAGTTGAGCTGGTGGAAGCCGTGTACGAGGACCTCGAGTTGGACTACCTAGGAGGAGATGGTGAGACGCATCTACGAGACACAAGGCA[C/T]
GCCATTATACTATAGCGCAAGCGGTACATCATCCTCCCTGGGCGACAAGCGGCGTCTCGTGCACCATCTCCTCCGGCTTCGCCGTCTCCTCCTGCACCAT

Allele Frequencies:

Populations	Population Size	Frequency of A(primary allele)	Frequency of G(secondary allele)	Frequency of N	Frequency of DEL	Frequency of others Allele
All	4726	76.80%	19.90%	2.09%	1.18%	NA
All Indica	2759	97.50%	1.00%	1.49%	0.00%	NA
All Japonica	1512	45.70%	50.30%	0.40%	3.64%	NA
Aus	269	51.30%	45.00%	3.72%	0.00%	NA
Indica I	595	98.20%	1.30%	0.50%	0.00%	NA
Indica II	465	99.10%	0.60%	0.22%	0.00%	NA
Indica III	913	96.20%	0.40%	3.40%	0.00%	NA
Indica Intermediate	786	97.60%	1.70%	0.76%	0.00%	NA
Temperate Japonica	767	13.20%	80.30%	0.00%	6.52%	NA
Tropical Japonica	504	93.30%	6.50%	0.20%	0.00%	NA
Japonica Intermediate	241	49.80%	46.10%	2.07%	2.07%	NA
VI/Aromatic	96	52.10%	8.30%	38.54%	1.04%	NA
Intermediate	90	66.70%	27.80%	5.56%	0.00%	NA

Allele Effect:

Var ID	Var	Locus	snpEff Annotation	CooVar Annotation	Chromatin Accessibility Score	PolyPhen-2 Effect	PolyPhen-2 Score	SIFT Effect	SIFT Score
vg1000621991	G -> A	LOC_Os10g01984.1	intron_variant ; MODIFIER	silent_mutation	Average:26.698; most accessible tissue: Callus, score: 39.851	N	N	N	N
vg1000621991	G -> DEL	N	N	silent_mutation	Average:26.698; most accessible tissue: Callus, score: 39.851	N	N	N	N

Putative Genotype-Phenotype Associations:

Var ID	LMM P-value	LR P-value	Trait	Subpopulation	Is leadSNP	Publication
vg1000621991	2.28E-16	2.16E-33	mr1300	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	6.32E-08	3.09E-12	mr1300	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	1.44E-13	1.22E-41	mr1310	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	1.49E-06	2.55E-12	mr1310	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	6.33E-20	4.58E-56	mr1926	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	2.67E-07	3.66E-14	mr1926	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	1.52E-08	5.57E-13	mr1959	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	2.90E-06	2.27E-08	mr1959	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	5.56E-19	1.01E-43	mr1310_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	8.62E-09	9.57E-18	mr1310_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	3.78E-07	NA	mr1530_2	All	YES	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	1.13E-08	7.39E-19	mr1959_2	All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg1000621991	NA	4.32E-10	mr1959_2	Jap_All	Not	Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251